Volume 11, Issue 7, Pages 983-994 (July 2018) Genome Analysis of the Ancient Tracheophyte Selaginella tamariscina Reveals Evolutionary Features Relevant to the Acquisition of Desiccation Tolerance  Zhichao Xu, Tianyi Xin, Dorothea Bartels, Ying Li, Wei Gu, Hui Yao, Sai Liu, Haoying Yu, Xiangdong Pu, Jianguo Zhou, Jiang Xu, Caicai Xi, Hetian Lei, Jingyuan Song, Shilin Chen  Molecular Plant  Volume 11, Issue 7, Pages 983-994 (July 2018) DOI: 10.1016/j.molp.2018.05.003 Copyright © 2018 The Author Terms and Conditions

Figure 1 Phenotype, Chlorophyll Fluorescence, and Photochemical Efficiency of S. tamariscina during Drought and Rehydration. (A) Chlorophyll fluorescence Y(II) measured using the MAXI version of the IMAGING-PAM M-Series fluorometer under HD (hydration, 1.49 g H2O g−1 dry weight [dwt]), 70% RWC (1.04 g H2O g−1 dwt), 50% RWC (0.75 g H2O g−1 dwt), 30% RWC (0.46 g H2O g−1 dwt), 15% RWC (0.22 g H2O g−1 dwt), 5% RWC (0.07 g H2O g−1 dwt), RH 2 h (rehydration, 1 g H2O g−1 dwt), RH 4 h (1.28 g H2O g−1 dwt), and RH 6 h (1.49 g H2O g−1 dwt). (B) The photochemical efficiency (Fv/Fm) of S. tamariscina during dehydration and rehydration. The maximum and mean Fv/Fm values represent the maximal and mean photochemical efficiencies, respectively. Molecular Plant 2018 11, 983-994DOI: (10.1016/j.molp.2018.05.003) Copyright © 2018 The Author Terms and Conditions

Figure 2 Evolutionary Analysis of the S. tamariscina Genome. (A) An ideogram showing the features of the 20y longest scaffolds from the S. tamariscina genome. The circus map shows, from outside to inside, the gene density, upregulated differentially expressed genes (DEGs), downregulated DEGS, transposable element density, and sequence similarity between S. tamariscina and S. moellendorffii. (B) Venn diagram illustrating the gene families and genes unique to S. tamariscina and those common to seven other plant genomes, including chlorophytes, mosses, lycophytes, and euphyllophytes. (C) Expansion and contraction of gene families among 18 plant species. Phylogenetic analysis of these 18 species was performed with 18 high-quality 1:1 single-copy orthologous genes. Divergence time was estimated based on the divergence time of P. trichocarpa–G. max (94–127 MYA), A. thaliana–G. raimondii (81–94 MYA), and S. tuberosum–S. lycopersicum (5.09–10.25 MYA). Green and red numbers indicate gene family contraction and expansion events, respectively. The pie charts show the proportion of expanded/contracted/remained gene families in each plant species. Molecular Plant 2018 11, 983-994DOI: (10.1016/j.molp.2018.05.003) Copyright © 2018 The Author Terms and Conditions

Figure 3 Gene Loss and Structural Rearrangement of the S. tamariscina Chloroplast Genome. (A) The complete chloroplast genome of S. tamariscina. (B) The complete chloroplast genome of S. moellendorffii. The red frames indicate the location of cp-ndh genes. (C) Mauve alignment of the entire chloroplast genomes of S. tamariscina, S. moellendorffii, and S. uncinata. (D) The differential expression (FPKM) of cp-ndh genes in S. moellendorffii under natural condition (SM-N), 50% RWC (SM-50, 1.02 g H2O g−1 dwt), and 100% RWC (SM-100, 2.06 g H2O g−1 dwt). Molecular Plant 2018 11, 983-994DOI: (10.1016/j.molp.2018.05.003) Copyright © 2018 The Author Terms and Conditions

Figure 4 Phylogenetic Analysis and Differential Expression of the Oleosin Genes under Dehydration. (A) Phylogenetic analysis of the oleosin gene family in S. tamariscina and 17 additional plant genomes. (B) The heatmap represents gene expression levels (log2 FPKM) under natural condition (ST-N), 50% RWC (ST-50), and 100% RWC (ST-100). (C) The differential expression (FPKM) of five oleosin genes under HD (hydration), 70% RWC, 50% RWC, 30% RWC, 15% RWC, 5% RWC, RH 2 h (rehydration), RH 4 h, and RH 6 h. Molecular Plant 2018 11, 983-994DOI: (10.1016/j.molp.2018.05.003) Copyright © 2018 The Author Terms and Conditions

Figure 5 The Evolution of the ROS Generation and Scavenging Mechanism from Chlorophytes to Land Plants. The different colors represent different ROS genes in 18 plant species. The red frame and asterisk show the significant differences in ROS generation gene numbers between S. tamariscina and S. moellendorffii. Molecular Plant 2018 11, 983-994DOI: (10.1016/j.molp.2018.05.003) Copyright © 2018 The Author Terms and Conditions

Figure 6 A Blueprint of the Resurrection Mechanism in S. tamariscina, including the ABA-Dependent Pathway, the ABA-Independent Pathway, and ROS Homeostasis, Determined via Comparative Genomics. The heatmap shows gene expression levels (log2 FPKM) under natural condition (ST-N), 50% RWC (ST-50), and 100% RWC (ST-100). The underlined numbers indicate the number of protein-coding genes in the S. tamariscina genome. Molecular Plant 2018 11, 983-994DOI: (10.1016/j.molp.2018.05.003) Copyright © 2018 The Author Terms and Conditions